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Sun P, Huang L, Xu D, Warren A, Huang B, Wang Y, Wang L, Xiao W, Kong J. Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea. Front Microbiol 2019; 10:2178. [PMID: 31616397 PMCID: PMC6768975 DOI: 10.3389/fmicb.2019.02178] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/05/2019] [Indexed: 12/20/2022] Open
Abstract
Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Liying Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lei Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Wupeng Xiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jie Kong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Malaterre C, Dussault AC, Rousseau-Mermans S, Barker G, Beisner BE, Bouchard F, Desjardins E, Handa IT, Kembel SW, Lajoie G, Maris V, Munson AD, Odenbaugh J, Poisot T, Shapiro BJ, Suttle CA. Functional Diversity: An Epistemic Roadmap. Bioscience 2019. [DOI: 10.1093/biosci/biz089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Functional diversity holds the promise of understanding ecosystems in ways unattainable by taxonomic diversity studies. Underlying this promise is the intuition that investigating the diversity of what organisms actually do (i.e., their functional traits) within ecosystems will generate more reliable insights into the ways these ecosystems behave, compared to considering only species diversity. But this promise also rests on several conceptual and methodological (i.e., epistemic) assumptions that cut across various theories and domains of ecology. These assumptions should be clearly addressed, notably for the sake of an effective comparison and integration across domains, and for assessing whether or not to use functional diversity approaches for developing ecological management strategies. The objective of this contribution is to identify and critically analyze the most salient of these assumptions. To this aim, we provide an epistemic roadmap that pinpoints these assumptions along a set of historical, conceptual, empirical, theoretical, and normative dimensions.
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Affiliation(s)
| | | | | | | | | | | | | | - I Tanya Handa
- Department of biological sciences, Université du Québec à Montréal
| | | | - Geneviève Lajoie
- Department of biological sciences, Université du Québec à Montréal
| | | | - Alison D Munson
- Département des sciences du bois et de la forêt, Université Laval, Canada
| | | | | | | | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, Department of Botany, Department of Microbiology and Immunology
- Institute for the Oceans and Fisheries at the University of British Columbia, Canada
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53
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Abraham JS, Sripoorna S, Maurya S, Makhija S, Gupta R, Toteja R. Techniques and tools for species identification in ciliates: a review. Int J Syst Evol Microbiol 2019; 69:877-894. [DOI: 10.1099/ijsem.0.003176] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a ‘total evidence’ approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.
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Affiliation(s)
- Jeeva Susan Abraham
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - S. Sripoorna
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, Bapu dham, Chanakyapuri, New Delhi 110021, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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Wirth C, Limberger R, Weisse T. Temperature × light interaction and tolerance of high water temperature in the planktonic freshwater flagellates Cryptomonas (Cryptophyceae) and Dinobryon (Chrysophyceae). JOURNAL OF PHYCOLOGY 2019; 55:404-414. [PMID: 30556585 PMCID: PMC6590229 DOI: 10.1111/jpy.12826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Using microcosm experiments, we investigated the interactive effects of temperature and light on specific growth rates of three species each of the phytoplanktonic genera Cryptomonas and Dinobryon. Several species of these genera play important roles in the food web of lakes and seem to be sensitive to high water temperature. We measured growth rates at three to four photon flux densities ranging from 10 to 240 μmol photon · m-2 · s-1 and at 4-5 temperatures ranging from 10°C to 28°C. The temperature × light interaction was generally strong, species specific, and also genus specific. Five of the six species studied tolerated 25°C when light availability was high; however, low light reduced tolerance of high temperatures. Growth rates of all six species were unaffected by temperature in the 10°C-15°C range at light levels ≤50 μmol photon · m-2 · s-1 . At high light, growth rates of Cryptomonas spp. increased with temperature until the temperature optimum was reached and then declined. The Dinobryon species were less sensitive than Cryptomonas spp. to photon flux densities of 40 μmol photon · m-2 · s-1 and 200 μmol photon · m-2 · s-1 over the entire temperature range but did not grow under a combination of very low light (10 μmol photon · m-2 · s-1 ) and high temperature (≥20°C). Among the three Cryptomonas species, cell volume declined with temperature and the maximum temperature tolerated was negatively related to cell size. Since Cryptomonas is important food for microzooplankton, these trends may affect the pelagic carbon flow if lake warming continues.
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Affiliation(s)
- Christina Wirth
- Research Department for LimnologyUniversity of InnsbruckMondseestr. 95310MondseeAustria
| | - Romana Limberger
- Research Department for LimnologyUniversity of InnsbruckMondseestr. 95310MondseeAustria
| | - Thomas Weisse
- Research Department for LimnologyUniversity of InnsbruckMondseestr. 95310MondseeAustria
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Nishigami Y, Ohmura T, Taniguchi A, Nonaka S, Manabe J, Ishikawa T, Ichikawa M. Influence of cellular shape on sliding behavior of ciliates. Commun Integr Biol 2018; 11:e1506666. [PMID: 30534342 PMCID: PMC6284593 DOI: 10.1080/19420889.2018.1506666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/18/2018] [Accepted: 07/25/2018] [Indexed: 11/03/2022] Open
Abstract
Some types of ciliates accumulate on solid/fluid interfaces. This behavior is advantageous to survival in nature due to the presence of sufficient nutrition and stable environments. Recently, the accumulating mechanisms of Tetrahymena pyriformis at the interface were investigated. The synergy of the ellipsoidal shape of the cell body and the mechanosensing feature of the cilia allow for cells to slide on interfaces, and the sliding behavior leads to cell accumulation on the interfaces. Here, to examine the generality of the sliding behavior of ciliates, we characterized the behavior of Paramecium caudatum, which is a commonly studied ciliate. Our experimental and numerical results confirmed that P. caudatum also slid on the solid/fluid interface by using the same mechanism as T. pyriformis. In addition, we evaluated the effects of cellular ellipticity on their behaviors near the wall with a phase diagram produced via numerical simulation.
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Affiliation(s)
| | - Takuya Ohmura
- Department of Physics, Kyoto University, Sakyo, Kyoto, Japan
| | - Atsushi Taniguchi
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki, Japan
| | - Shigenori Nonaka
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki, Japan
| | - Junichi Manabe
- Graduate School of Engineering, Tohoku University, Aoba, Sendai, Japan
| | - Takuji Ishikawa
- Graduate School of Engineering, Tohoku University, Aoba, Sendai, Japan
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Xu Y, Stoeck T, Forster D, Ma Z, Zhang L, Fan X. Environmental status assessment using biological traits analyses and functional diversity indices of benthic ciliate communities. MARINE POLLUTION BULLETIN 2018; 131:646-654. [PMID: 29886992 DOI: 10.1016/j.marpolbul.2018.04.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/10/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
In this study, we tested the hypothesis that the functional diversity of benthic ciliates has high potential to monitor marine ecological status. Therefore, we investigated the spatial and temporal variation of functional diversity of benthic ciliates in the Yangtze Estuary during one year using biological traits analyses and functional diversity indices. Traits and community compositions showed clear spatial and temporal variations. Among a variety of biological traits, feeding type and body size emerged as strongest predictable variables. Functional divergence (FDiv) had an advantage over two other functional diversity indices, as well as over classical diversity measures (i.e. richness, evenness, Shannon-Wiener) to infer environmental status. Significant correlations between biological traits, FDiv and environmental variables (i.e. nutrients, temperature, salinity) suggested that functional diversity of benthic ciliates might be used as a bio-indicator in environmental status assessments. Further mandatory researches need to implement functional diversity of ciliates in routine monitoring programs were discussed.
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Affiliation(s)
- Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Thorsten Stoeck
- University of Kaiserslautern, Ecology Group, Erwin Schroedinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Dominik Forster
- University of Kaiserslautern, Ecology Group, Erwin Schroedinger Str. 14, D-67663 Kaiserslautern, Germany
| | - Zuhang Ma
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Liquan Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai 200241, China.
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Meng Z, Xu K, Dai R, Warren A. Benthic ciliate diversity and community composition along water depth gradients: a comparison between the intertidal and offshore areas. Eur J Protistol 2018; 65:31-41. [PMID: 29807311 DOI: 10.1016/j.ejop.2018.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 11/15/2022]
Abstract
The diversity of marine benthic ciliates is largely known from the intertidal zone. No comparative data are available for the change of ciliate communities from the intertidal to offshore sediments in the Yellow Sea. We investigated the community composition and diversity of benthic ciliates at two intertidal (sandy and silty-sand) stations and eight offshore stations along a latitudinal transect in the Yellow Sea. The ciliate abundance and biomass decreased almost linearly with increasing water depth and distance from the intertidal zone. Diversity indices showed a similar trend. By contrast, the total species richness and taxonomic diversity were much higher in the offshore sediments than in the intertidal area. Among the total of 94 species identified, only 20 species were shared by the two habitats, which were characterized by different dominant ciliate assemblages. Carnivorous ciliates always constituted the primary feeding type in terms of biomass at all offshore stations and the intertidal sandy station, whereas at the intertidal silty-sand station the primary feeding group varied throughout the period of sampling. Multivariate analyses indicates the ciliate communities were significantly different between the two habitats. Bottom water temperature and sediment grain size were the key factors that explained the ciliate community structure.
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Affiliation(s)
- Zhaocui Meng
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Renhai Dai
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; National Oceanographic Center, Qingdao 266071, China
| | - Alan Warren
- Dept. Life Sciences, Natural History Museum,Cromwell Road, London, SW7 5BD, UK
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Abstract
Single-celled microorganisms are important in ecosystems, and their behaviors impact the Earth’s environments. To survive in harsh environments, these organisms frequently act as though exercising discretion. How do they achieve such intelligent behaviors? In this work, we focused on the accumulation of ciliates on solid/fluid interfaces, where they can obtain sufficient nutrients and a stable environment. This phenomenon is not described in the standard hydrodynamics of microswimmers. Our experiment and simulation revealed that simple principles, the anisotropic shape of the cell and the mechanosensing nature of cilia, induce the accumulation of ciliates on solid/fluid interfaces. The contribution of our work is that a simple response of the cellular apparatus and fluid dynamics explain the apparently clever behavior of ciliates. An important habit of ciliates, namely, their behavioral preference for walls, is revealed through experiments and hydrodynamic simulations. A simple mechanical response of individual ciliary beating (i.e., the beating is stalled by the cilium contacting a wall) can solely determine the sliding motion of the ciliate along the wall and result in a wall-preferring behavior. Considering ciliate ethology, this mechanosensing system is likely an advantage in the single cell’s ability to locate nutrition. In other words, ciliates can skillfully use both the sliding motion to feed on a surface and the traveling motion in bulk water to locate new surfaces according to the single “swimming” mission.
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